Summary of Study ST002060
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001304. The data can be accessed directly via it's Project DOI: 10.21228/M8570V This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002060 |
| Study Title | Pollen metabolomics using Arabidopsis thaliana: Comparison of pollen at mature, hydration and germination stage |
| Study Type | Untargeted Metabolomics |
| Study Summary | In this study, we investigated the differential metabolic pathway enrichment among mature, hydrated, and germinated pollen using untargeted metabolomics analysis. Integration of publicly available transcriptome with presented metabolome data revealed starch and sucrose metabolism was significantly increased during pollen hydration and germination. The alterations in central metabolism focusing on sugar, fatty acids, and lipids were analyzed in detail. Several metabolites, including palmitic acid, oleic acid, linolenic acid, quercetin, luteolin/kaempferol, and γ-aminobutyric acid (GABA), were elevated in the hydrated pollen, suggesting a potential role in activating pollen tube emergence. The metabolite levels of mature, hydrated, and germinated pollen, presented in this work provide insights on the molecular basis of pollen germination. |
| Institute | University of Illinois Urbana-Champaign |
| Department | Department of Plant Biology |
| Laboratory | Li-Qing Chen Lab |
| Last Name | Kambhampati |
| First Name | Shrikaar |
| Address | 975 North Warson Road, St. Louis, MO 63132 |
| shrikaar.k@gmail.com | |
| Phone | 3144025550 |
| Submit Date | 2022-01-17 |
| Num Groups | 3 |
| Total Subjects | 12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-02-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Sample Preparation:
| Sampleprep ID: | SP002148 |
| Sampleprep Summary: | Total metabolites from pollen were extracted using a phase separation method previously described (Kambhampati et al., 2021) with slight modifications. Briefly, 20-30 mg pollen tissue, collected in Eppendorf tubes, was extracted using 700 µL of chilled 7:3 (v/v) methanol: chloroform spiked with 50 µM each of 1.4-piperazinediethanesulfonic acid (PEPES), ribitol, and norvaline as internal standards. After two metal beads were also added to the samples, they were homogenized using a Tissue-Lyser for 5 min at 30 Hz. The samples were incubated on a rotary shaker at 4°C for 2 hours after which 300 µL ddH2O was added. The samples were then centrifuged at 14,000 rpm for 10 min to achieve phase separation and the upper aqueous phase, as well as the lower organic phase, were collected separately. The aqueous phases containing polar and nonpolar metabolites were split into two equal parts and dried using a speed vacuum centrifuge (Labconco®, Kansas City, USA). The two dried parts were re-suspended in 50 µL 80% (v/v) methanol, and 30 % (v/v) methanol for metabolomics analyses using hydrophilic interaction (HILIC) and reverse phase chromatography (RPLC), respectively. The organic phase was also dried using a speed vacuum centrifuge and re-suspended in 50 µL of 49:49:2 (v/v/v) mixture of acetonitrile: methanol: chloroform. All samples were filtered using a 0.8 µM PES membrane centrifuge filter (Sartorius, Goettingen, Germany) and transferred to a glass vial for injection into an LC-MS/MS system. |
| Sampleprep Protocol Filename: | Total_Metabolite_Extraction.docx |
| Processing Storage Conditions: | -80℃ |
